The term has come to mean any book not published by Marvel or DC comics. As they control about 80% of the market, I think that is an apt description.
I find that there is a lot of gold in this segment of the market and a great deal of reluctance for many fans to try the material . I'm not sure why it is so hard to get a lot more people interested in independent books, because as a group comic fans are usually a little more open to new ideas.
Having said that there is still a lot of crap in the independent market and some pornographic material in some of these comics. Plus the independent market may start a trend (Zombie comics), but then be just as guilty of over doing that same theme.
Part in an effort to at least give mention to what I think are some really good independent books I offer the following:
Mouse Guard - The mini-series ended today and is fresh in my mind. I believe David Peterson plans to do another mini-series. This book has the quality of being a children's book that can be enjoyed by adults. Also it contains a darker feel to then many of the namby pamby kids books that seem to be the bulk of what is being written for kids today. A great book and deserving of wide spread sales.
X-Isle - A mini-series about a mysterious island that our ship wrecked survivors find themselves on. A little bit of Lost, HG Wells and monster movie all rolled into one. An enjoyable read.
Meltdown - A 2 part series that is already over. An examination of a hero whose powers are killing him and what he does with the rest of his life.
Invincible - The best super hero book on the market today. Reminds me of how Spider-Man was through the first 38 issues of his run with Lee/Ditko. The character is growing and moving on. At the same time it is also very modern in how Kirkman builds his sub-plots over months and months before bringing them to fruition.
30 Days of Night - Already a wealth of material. Steve Niles and Ben Templesmith's Zombie tales. This series now has moved past the originators but is still developing good tales of Zombies. Most of the material is available in trade form and well worth your time.
Local - I believe we are halfway through this 12 part saga. Every issue takes place in a different town and every issue the main character Megan is another year older. A really nice piece exploring someone who is lost and trying to find themselves.
Wormwood Gentlemen Corpse - Ben Templesmith as artist and writer about a worm that inhabits a corpse and his adventures. Insane sounding, but really a strong artistic showing and some really fun over the top stories.
Thrud- Conan on steroids and with the IQ of a tree stump. Just pure out and out humor in a barbaric way.
Enigma Cipher - A great mystery that starts with a WWII secret and then spirals off into an adventure of a normal girl caught in an extraordinary situation. All her friends have been killed and she is not even sure what it is they have discovered. Great thriller.
Desperadoes: Buffalo Dreams - Western and supernatural adventure all rolled into one. This has been a series of mini-series that has been building character as well as telling stories. Another book really worth the look.
If you include Vertigo and Icon you can add Crossing Midnight, American Virgin, Criminal, Exterminators, Testament and others to the list. Hell I even left off Fell and Goon which are two terrific series.
A lot of gold but you have to look for it, but the rewards are great. Especially when you realize how much is out there and often it can be pick up for a song on e-bay or wait for at sale at your local comic shop or favorite internet store.